distanceToNearest is going to return a distance, which is always going to
be absolute. If you want to make things positive and negative, then you
will need to call precede and follow and perform a similar calculation. As
long as you have the TSSs in a GRanges, this should work fine. There is no
need for a TranscriptDb.

Michael

On Tue, Aug 21, 2012 at 8:29 AM, d r <dolevrahat@gmail.com> wrote:

> Hello
>
> I want to calculate the distance between HumanMethylation450k probes
> and their nearest TSS using refseq hg19 genes, in such a way that if
> the probe is downstream from the TSS the distance will be assigned a
> positive value, and if the probe is upstream from the TSS, the
> distance will be assigned a negative value. The idea is that both
> strands will be considered.
>
> The distance is to be positive if the nearest TSS is either on the '+
> strand and its coordinate is greater than the probe's, or of the
> nearest TSS is on the '-' strand and its coordinate is smaller than
> the probe's.
>
> likewise, the distance is to be negative if the nearest TSS is on the
> '+' strand and its coordinate is smaller than the probe's or on the
> '-' strand and its coordinate is grater then the probe's.
>
> It may be possible to do this with transcripts(), but unfortunately my
> dat is not on TranscriptDb
> <http://127.0.0.1:37980/help/library/GenomicFeatures/help/TranscriptDb>
> objects.
>
> Is there a way to this using the distanceToNearest method of GRanges?
>
>
>
> thanks
>
> Dolev Rahat
>
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